GapMind for catabolism of small carbon sources

 

Aligments for a candidate for badK in Azospirillum brasilense Sp245

Align BadK (characterized)
to candidate AZOBR_RS26485 AZOBR_RS26485 enoyl-CoA hydratase

Query= metacyc::MONOMER-943
         (258 letters)



>lcl|FitnessBrowser__azobra:AZOBR_RS26485 AZOBR_RS26485 enoyl-CoA
           hydratase
          Length = 262

 Score =  167 bits (422), Expect = 3e-46
 Identities = 108/257 (42%), Positives = 139/257 (54%), Gaps = 7/257 (2%)

Query: 5   PILTETQGRVGIITLNRPDVLNALNDALMDALGGALLAFDADDGIGAIVIAG-NTRAFAA 63
           PILT   G VG+IT+NRP  LNAL+   +  L  AL   ++DDG+  IV+ G   RAF A
Sbjct: 6   PILTSRDGAVGLITINRPTTLNALDVPTLLELERALGELESDDGVHVIVVTGAGERAFVA 65

Query: 64  GADIASMAAWS----YSDVYGSNFITRNWETIRQIRKPVLAAVAGLAYGGGCELALACDI 119
           G DIA + +      Y D   +  + R +       KP +AAV G A GGG EL L+ DI
Sbjct: 66  GGDIADLDSRQGLAHYLDF--AEVVHRVFRRFETCDKPTIAAVNGWALGGGTELVLSLDI 123

Query: 120 VIAGRSAKFALPEIKLGLLPGAGGTQRLPRAIGKAKAMDMCLSARPLNAEEADRYGLVSR 179
            IA  +AKF LPEI LGL PGAGGTQR+ R I   +A ++  +     A EA  +GLV+R
Sbjct: 124 RIAADTAKFGLPEINLGLFPGAGGTQRILRQIPPCRARELVFTGDQFTAAEAVAWGLVNR 183

Query: 180 VVDDDRLRDETVALATTIAAFSAPALMALKESLNRAFESTLAEGILFERRELHARFASAD 239
            V    L  E +A A  IAA S   L   K +L    E  L   + +E+  +     S D
Sbjct: 184 AVPKADLMAEAMATAQKIAAKSPLILKLTKRTLRHGAEMPLGASLAYEQAMIGLVLDSQD 243

Query: 240 AREGIQAFLEKRAPCFS 256
           A EG +AFLEKR   F+
Sbjct: 244 AHEGCRAFLEKRKAAFT 260


Lambda     K      H
   0.321    0.135    0.389 

Gapped
Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 1
Number of Hits to DB: 138
Number of extensions: 4
Number of successful extensions: 3
Number of sequences better than 1.0e-02: 1
Number of HSP's gapped: 1
Number of HSP's successfully gapped: 1
Length of query: 258
Length of database: 262
Length adjustment: 24
Effective length of query: 234
Effective length of database: 238
Effective search space:    55692
Effective search space used:    55692
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.9 bits)
S2: 47 (22.7 bits)

This GapMind analysis is from Sep 17 2021. The underlying query database was built on Sep 17 2021.

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About GapMind

Each pathway is defined by a set of rules based on individual steps or genes. Candidates for each step are identified by using ublast (a fast alternative to protein BLAST) against a database of manually-curated proteins (most of which are experimentally characterized) or by using HMMer with enzyme models (usually from TIGRFam). Ublast hits may be split across two different proteins.

A candidate for a step is "high confidence" if either:

where "other" refers to the best ublast hit to a sequence that is not annotated as performing this step (and is not "ignored").

Otherwise, a candidate is "medium confidence" if either:

Other blast hits with at least 50% coverage are "low confidence."

Steps with no high- or medium-confidence candidates may be considered "gaps." For the typical bacterium that can make all 20 amino acids, there are 1-2 gaps in amino acid biosynthesis pathways. For diverse bacteria and archaea that can utilize a carbon source, there is a complete high-confidence catabolic pathway (including a transporter) just 38% of the time, and there is a complete medium-confidence pathway 63% of the time. Gaps may be due to:

GapMind relies on the predicted proteins in the genome and does not search the six-frame translation. In most cases, you can search the six-frame translation by clicking on links to Curated BLAST for each step definition (in the per-step page).

For more information, see the paper from 2019 on GapMind for amino acid biosynthesis, the paper from 2022 on GapMind for carbon sources, or view the source code.

If you notice any errors or omissions in the step descriptions, or any questionable results, please let us know

by Morgan Price, Arkin group, Lawrence Berkeley National Laboratory